Next Tuesday at 2024-12-10 18:00 CET, we will hold the last community meeting of the year!
@lukasheumos.bsky.social will talk about pertpy, a Python-based modular framework for the analysis of large-scale perturbation single-cell experiments. The GitHub repo: github.com/scverse/pertpy
@lukasheumos.bsky.social will talk about pertpy, a Python-based modular framework for the analysis of large-scale perturbation single-cell experiments. The GitHub repo: github.com/scverse/pertpy
GitHub - scverse/pertpy: Perturbation Analysis in the scverse ecosystem.
Perturbation Analysis in the scverse ecosystem. Contribute to scverse/pertpy development by creating an account on GitHub.
github.com
December 3, 2024 at 9:56 AM
Next Tuesday at 2024-12-10 18:00 CET, we will hold the last community meeting of the year!
@lukasheumos.bsky.social will talk about pertpy, a Python-based modular framework for the analysis of large-scale perturbation single-cell experiments. The GitHub repo: github.com/scverse/pertpy
@lukasheumos.bsky.social will talk about pertpy, a Python-based modular framework for the analysis of large-scale perturbation single-cell experiments. The GitHub repo: github.com/scverse/pertpy
Explore the scverse Starter Pack!
Stay informed about the latest scverse events, software updates, and community news. Everything you need to know about foundational tools for single-cell omics analysis in one place.
go.bsky.app/UvFMa8d
Stay informed about the latest scverse events, software updates, and community news. Everything you need to know about foundational tools for single-cell omics analysis in one place.
go.bsky.app/UvFMa8d
November 16, 2024 at 1:59 PM
Explore the scverse Starter Pack!
Stay informed about the latest scverse events, software updates, and community news. Everything you need to know about foundational tools for single-cell omics analysis in one place.
go.bsky.app/UvFMa8d
Stay informed about the latest scverse events, software updates, and community news. Everything you need to know about foundational tools for single-cell omics analysis in one place.
go.bsky.app/UvFMa8d
I'm convinced that any python development should farm out I/O to rust backends. I've seen considerable speedup switching from pandas to polars, and similar gains for custom containers using.
Another good example of this is the github.com/scverse/annb... implementation which uses a zarr backend.
Another good example of this is the github.com/scverse/annb... implementation which uses a zarr backend.
GitHub - scverse/annbatch: Minibatch loading for on-disk anndata files, co-developed by Lamin Labs and scverse
Minibatch loading for on-disk anndata files, co-developed by Lamin Labs and scverse - scverse/annbatch
github.com
May 12, 2026 at 3:52 PM
I'm convinced that any python development should farm out I/O to rust backends. I've seen considerable speedup switching from pandas to polars, and similar gains for custom containers using.
Another good example of this is the github.com/scverse/annb... implementation which uses a zarr backend.
Another good example of this is the github.com/scverse/annb... implementation which uses a zarr backend.
scverse conference 2025 done ✅ Really engaging week at Stanford with scPerturb-seq work, agentic models in biology, and strong interest in scaling software to millions of cells. Organizing alongside the rest of the @scverse.bsky.social team was a blast! Hope attendees found it productive 😄
November 21, 2025 at 5:37 PM
scverse conference 2025 done ✅ Really engaging week at Stanford with scPerturb-seq work, agentic models in biology, and strong interest in scaling software to millions of cells. Organizing alongside the rest of the @scverse.bsky.social team was a blast! Hope attendees found it productive 😄
The @chanzuckerberg.bsky.social Cell Science Meeting in Chicago just concluded. I had the opportunity to present the latest advancements in spatial omics within the #scverse ecosystem, highlighting our efforts to scale our infrastructure in preparation for the datasets of tomorrow.
April 15, 2025 at 2:52 AM
The @chanzuckerberg.bsky.social Cell Science Meeting in Chicago just concluded. I had the opportunity to present the latest advancements in spatial omics within the #scverse ecosystem, highlighting our efforts to scale our infrastructure in preparation for the datasets of tomorrow.
Proteomics analysis has always lived in its own universe. AlphaPeptTools puts it in #scverse instead, so that proteome, transcriptome and spatial data live in one ecosystem. 11 search engines (DDA+DIA) read in, proteomics-specific statistics, #scverse native.
doi.org/10.64898/202...
doi.org/10.64898/202...
September 15, 2026 at 9:25 AM
Proteomics analysis has always lived in its own universe. AlphaPeptTools puts it in #scverse instead, so that proteome, transcriptome and spatial data live in one ecosystem. 11 search engines (DDA+DIA) read in, proteomics-specific statistics, #scverse native.
doi.org/10.64898/202...
doi.org/10.64898/202...
✍️ New Bioconductor blog post on the SpatialData hackathon and workshop, organized by https://buff.ly/4j1UidT with Bioconductor participation. Check it out: https://buff.ly/4fM1qrH
Thanks @arturmansl.bsky.social !
#Bioconductor #SpatialData #scverse #Bioinformatics #OpenScience #RStats
Thanks @arturmansl.bsky.social !
#Bioconductor #SpatialData #scverse #Bioinformatics #OpenScience #RStats
2024 SpatialData Workshop – Bioconductor community blog
R/Bioconductor developers participating in the 1st scverse SpatialData Workshop
buff.ly
January 9, 2025 at 12:11 PM
✍️ New Bioconductor blog post on the SpatialData hackathon and workshop, organized by https://buff.ly/4j1UidT with Bioconductor participation. Check it out: https://buff.ly/4fM1qrH
Thanks @arturmansl.bsky.social !
#Bioconductor #SpatialData #scverse #Bioinformatics #OpenScience #RStats
Thanks @arturmansl.bsky.social !
#Bioconductor #SpatialData #scverse #Bioinformatics #OpenScience #RStats
Meet the keynote speakers for the 2025 scverse conference!
Elham Azizi, Associate Professor of Cancer Data Research and Biomedical Engineering at Columbia University
🧵
@elhamazizi.bsky.social
@columbiauniversity.bsky.social
#scverse #scverse2025 #machinelearning #genomics #cancerimmunology
Elham Azizi, Associate Professor of Cancer Data Research and Biomedical Engineering at Columbia University
🧵
@elhamazizi.bsky.social
@columbiauniversity.bsky.social
#scverse #scverse2025 #machinelearning #genomics #cancerimmunology
August 28, 2025 at 3:04 PM
Meet the keynote speakers for the 2025 scverse conference!
Elham Azizi, Associate Professor of Cancer Data Research and Biomedical Engineering at Columbia University
🧵
@elhamazizi.bsky.social
@columbiauniversity.bsky.social
#scverse #scverse2025 #machinelearning #genomics #cancerimmunology
Elham Azizi, Associate Professor of Cancer Data Research and Biomedical Engineering at Columbia University
🧵
@elhamazizi.bsky.social
@columbiauniversity.bsky.social
#scverse #scverse2025 #machinelearning #genomics #cancerimmunology
If you are considering creating a Python package I strongly suggest cookiecutter-scverse by @scverse.bsky.social
It’s a template that already incorporates many useful features.
github.com/scverse/cook...
It’s a template that already incorporates many useful features.
github.com/scverse/cook...
November 25, 2024 at 4:51 PM
If you are considering creating a Python package I strongly suggest cookiecutter-scverse by @scverse.bsky.social
It’s a template that already incorporates many useful features.
github.com/scverse/cook...
It’s a template that already incorporates many useful features.
github.com/scverse/cook...
🚀 Excited to share scPortrait! Led by Sophia Mädler & Niklas Schmacke w/ the Mann lab — a new @scverse tool for standardized single-cell image data. Enables ML-ready extraction, >1B cell processing, cross-omics, & cancer macrophage insights.
🔗 www.biorxiv.org/content/10.1...
🔗 www.biorxiv.org/content/10.1...
September 28, 2025 at 5:50 PM
🚀 Excited to share scPortrait! Led by Sophia Mädler & Niklas Schmacke w/ the Mann lab — a new @scverse tool for standardized single-cell image data. Enables ML-ready extraction, >1B cell processing, cross-omics, & cancer macrophage insights.
🔗 www.biorxiv.org/content/10.1...
🔗 www.biorxiv.org/content/10.1...
While we are still working on the first feature/perf full release of the rustar-aligner, you can currently use the main branch to build a byte-compatible STAR index >2x faster with <1/2 of the RAM (and use it with STAR). Plus it fixes a small STAR bug github.com/scverse/rust...
GitHub - scverse/rustar-aligner: A rust implementation of STAR
A rust implementation of STAR. Contribute to scverse/rustar-aligner development by creating an account on GitHub.
github.com
August 27, 2026 at 3:20 PM
While we are still working on the first feature/perf full release of the rustar-aligner, you can currently use the main branch to build a byte-compatible STAR index >2x faster with <1/2 of the RAM (and use it with STAR). Plus it fixes a small STAR bug github.com/scverse/rust...
scverse conference 2026 will take place in Copenhagen, October 12–14. ✨
Three days of all-things-single-cell and open-source tooling and community in real life.
More details soon but for now, mark your calendars.
scverse.org/conference20...
See you in Copenhagen 🇩🇰
Three days of all-things-single-cell and open-source tooling and community in real life.
More details soon but for now, mark your calendars.
scverse.org/conference20...
See you in Copenhagen 🇩🇰
scverse conference 2026
scverse.org
May 27, 2026 at 7:07 PM
scverse conference 2026 will take place in Copenhagen, October 12–14. ✨
Three days of all-things-single-cell and open-source tooling and community in real life.
More details soon but for now, mark your calendars.
scverse.org/conference20...
See you in Copenhagen 🇩🇰
Three days of all-things-single-cell and open-source tooling and community in real life.
More details soon but for now, mark your calendars.
scverse.org/conference20...
See you in Copenhagen 🇩🇰
Excited to share new preprint with NVIDIA on GPU-accelerated single-cell analysis 🚀
rapids-singlecell brings native GPU support to scverse/AnnData: hours → seconds (1M cells: ~52m → ~25s), scaling to 100M cells. Huge thanks to Severin Dicks 🙌
📄 arxiv.org/abs/2603.02402
rapids-singlecell brings native GPU support to scverse/AnnData: hours → seconds (1M cells: ~52m → ~25s), scaling to 100M cells. Huge thanks to Severin Dicks 🙌
📄 arxiv.org/abs/2603.02402
March 17, 2026 at 8:16 AM
Excited to share new preprint with NVIDIA on GPU-accelerated single-cell analysis 🚀
rapids-singlecell brings native GPU support to scverse/AnnData: hours → seconds (1M cells: ~52m → ~25s), scaling to 100M cells. Huge thanks to Severin Dicks 🙌
📄 arxiv.org/abs/2603.02402
rapids-singlecell brings native GPU support to scverse/AnnData: hours → seconds (1M cells: ~52m → ~25s), scaling to 100M cells. Huge thanks to Severin Dicks 🙌
📄 arxiv.org/abs/2603.02402
Closing 2024, scverse celebrates growth and collaboration! Huge thanks to everyone on this journey and our core team & board (@fabiantheis.bsky.social, @francescafinotello.bsky.social, @steglelab.bsky.social, Nir Yosef, @panosroussos.bsky.social, @robp.bsky.social). Here's to an inspiring 2025!
December 19, 2024 at 10:17 AM
Closing 2024, scverse celebrates growth and collaboration! Huge thanks to everyone on this journey and our core team & board (@fabiantheis.bsky.social, @francescafinotello.bsky.social, @steglelab.bsky.social, Nir Yosef, @panosroussos.bsky.social, @robp.bsky.social). Here's to an inspiring 2025!
🔧 decoupler 2.0.6 is out thanks to @paubadiam.bsky.social, now as a core @scverse.bsky.social package scverse.org
This release includes a streamlined API aligned with scverse standards, updated vignettes, and a new one on pseudotime enrichment analysis 👇
decoupler.readthedocs.io/en/latest/
This release includes a streamlined API aligned with scverse standards, updated vignettes, and a new one on pseudotime enrichment analysis 👇
decoupler.readthedocs.io/en/latest/
June 12, 2025 at 6:36 AM
🔧 decoupler 2.0.6 is out thanks to @paubadiam.bsky.social, now as a core @scverse.bsky.social package scverse.org
This release includes a streamlined API aligned with scverse standards, updated vignettes, and a new one on pseudotime enrichment analysis 👇
decoupler.readthedocs.io/en/latest/
This release includes a streamlined API aligned with scverse standards, updated vignettes, and a new one on pseudotime enrichment analysis 👇
decoupler.readthedocs.io/en/latest/
📣 Mark your calendars! The 2025 edition of the scverse conference will take place on 17-19 November at Stanford University (US) scverse.org/conference20...
Call for abstracts and registrations coming soon!
Call for abstracts and registrations coming soon!
scverse conference 2025
Follow us on our channels to learn more details in the coming weeks
scverse.org
May 12, 2025 at 10:47 PM
📣 Mark your calendars! The 2025 edition of the scverse conference will take place on 17-19 November at Stanford University (US) scverse.org/conference20...
Call for abstracts and registrations coming soon!
Call for abstracts and registrations coming soon!
🧫 Meet the keynote speakers for the 2025 scverse conference!
Erika Alden DeBenedictis, Co-founder of The Align Foundation & CEO of Pioneer Labs
@erika-alden.bsky.social
@alignbio.bsky.social
@pioneerlabs.bsky.social
#scverse #scverse2025 #StructuralBiology #Biotech #Stanford
Erika Alden DeBenedictis, Co-founder of The Align Foundation & CEO of Pioneer Labs
@erika-alden.bsky.social
@alignbio.bsky.social
@pioneerlabs.bsky.social
#scverse #scverse2025 #StructuralBiology #Biotech #Stanford
August 26, 2025 at 2:36 PM
🧫 Meet the keynote speakers for the 2025 scverse conference!
Erika Alden DeBenedictis, Co-founder of The Align Foundation & CEO of Pioneer Labs
@erika-alden.bsky.social
@alignbio.bsky.social
@pioneerlabs.bsky.social
#scverse #scverse2025 #StructuralBiology #Biotech #Stanford
Erika Alden DeBenedictis, Co-founder of The Align Foundation & CEO of Pioneer Labs
@erika-alden.bsky.social
@alignbio.bsky.social
@pioneerlabs.bsky.social
#scverse #scverse2025 #StructuralBiology #Biotech #Stanford
The case study covers rustar-aligner (a re-write of STAR into rust), svb (a streamvbyte+VBZ/EX-ZD codec for signal compression), and kuva (scientific plotting library in rust
github.com/scverse/rust...
github.com/Psy-Fer/svb
github.com/Psy-Fer/kuva
github.com/scverse/rust...
github.com/Psy-Fer/svb
github.com/Psy-Fer/kuva
GitHub - scverse/rustar-aligner: A rust implementation of STAR
A rust implementation of STAR. Contribute to scverse/rustar-aligner development by creating an account on GitHub.
github.com
July 29, 2026 at 1:40 AM
The case study covers rustar-aligner (a re-write of STAR into rust), svb (a streamvbyte+VBZ/EX-ZD codec for signal compression), and kuva (scientific plotting library in rust
github.com/scverse/rust...
github.com/Psy-Fer/svb
github.com/Psy-Fer/kuva
github.com/scverse/rust...
github.com/Psy-Fer/svb
github.com/Psy-Fer/kuva
🎉scverse conference 2025 Call for Abstracts DEADLINE EXTENDED! 🎉
We're excited to announce that the deadline to submit abstracts for the scverse Conference 2025 has been extended to September 15, 2025!
🧵
#scverse #scverse2025 #SingleCell #Conference
We're excited to announce that the deadline to submit abstracts for the scverse Conference 2025 has been extended to September 15, 2025!
🧵
#scverse #scverse2025 #SingleCell #Conference
September 1, 2025 at 4:18 PM
🎉scverse conference 2025 Call for Abstracts DEADLINE EXTENDED! 🎉
We're excited to announce that the deadline to submit abstracts for the scverse Conference 2025 has been extended to September 15, 2025!
🧵
#scverse #scverse2025 #SingleCell #Conference
We're excited to announce that the deadline to submit abstracts for the scverse Conference 2025 has been extended to September 15, 2025!
🧵
#scverse #scverse2025 #SingleCell #Conference
Want to contribute to the scverse omics ecosystem? Join the NVIDIA and scverse Hackathon: Accelerate Omics Workflows! Collaborate with NVIDIA experts, GPU-accelerated tools, and the scverse community. Apply by Aug 27, 2025. #Omics #DataScience #Hackathon #GPU
LINK: buff.ly/OCUdlks
LINK: buff.ly/OCUdlks
NVIDIA Accelerate Omics Hackathon
Take Omics tools to the next level with GPU acceleration.
buff.ly
August 14, 2025 at 3:06 PM
Want to contribute to the scverse omics ecosystem? Join the NVIDIA and scverse Hackathon: Accelerate Omics Workflows! Collaborate with NVIDIA experts, GPU-accelerated tools, and the scverse community. Apply by Aug 27, 2025. #Omics #DataScience #Hackathon #GPU
LINK: buff.ly/OCUdlks
LINK: buff.ly/OCUdlks
I am Stoked about our upcoming @scverse.bsky.social
and @owkin.bsky.social hackathon, focused on spatial omics data analysis.
📅 March 17-19, 2025
📍 Owkin office, Paris
Apply now: docs.google.com/forms/d/e/1F...
and @owkin.bsky.social hackathon, focused on spatial omics data analysis.
📅 March 17-19, 2025
📍 Owkin office, Paris
Apply now: docs.google.com/forms/d/e/1F...
Scverse x Owkin Hackathon in Paris
We're pleased to announce the next Scverse Hackathon will take place in the Owkin offices in Paris from 17/03/2025 9am to 19/03/2025 1:30pm.
This hackathon is a joint initiative between the scverse c...
docs.google.com
January 17, 2025 at 10:34 AM
I am Stoked about our upcoming @scverse.bsky.social
and @owkin.bsky.social hackathon, focused on spatial omics data analysis.
📅 March 17-19, 2025
📍 Owkin office, Paris
Apply now: docs.google.com/forms/d/e/1F...
and @owkin.bsky.social hackathon, focused on spatial omics data analysis.
📅 March 17-19, 2025
📍 Owkin office, Paris
Apply now: docs.google.com/forms/d/e/1F...
🚀 NEW PANEL ANNOUNCEMENT: Agentic Workflows in Bioinformatics at scverse 2025! 🚀
We're thrilled to introduce an exciting panel discussion at the upcoming scverse Conference 2025!
More information in 🧵
#scverse2025 #Bioinformatics #AgenticAI #Conference
We're thrilled to introduce an exciting panel discussion at the upcoming scverse Conference 2025!
More information in 🧵
#scverse2025 #Bioinformatics #AgenticAI #Conference
October 3, 2025 at 3:43 PM
🚀 NEW PANEL ANNOUNCEMENT: Agentic Workflows in Bioinformatics at scverse 2025! 🚀
We're thrilled to introduce an exciting panel discussion at the upcoming scverse Conference 2025!
More information in 🧵
#scverse2025 #Bioinformatics #AgenticAI #Conference
We're thrilled to introduce an exciting panel discussion at the upcoming scverse Conference 2025!
More information in 🧵
#scverse2025 #Bioinformatics #AgenticAI #Conference
anndataR enables seamless R-Python interoperability for single-cell RNA-seq by reading, writing, and converting H5AD files, supporting Seurat and SingleCellExperiment formats www.biorxiv.org/content/10.1... 🧬🖥️🧪 #Rstats github.com/scverse/annd...
August 29, 2025 at 10:15 AM
anndataR enables seamless R-Python interoperability for single-cell RNA-seq by reading, writing, and converting H5AD files, supporting Seurat and SingleCellExperiment formats www.biorxiv.org/content/10.1... 🧬🖥️🧪 #Rstats github.com/scverse/annd...
New preprint out!
We introduce 𝐬𝐩𝐚𝐭𝐢𝐚𝐥𝐩𝐫𝐨𝐭𝐞𝐨𝐦𝐢𝐜𝐬, a Python package for end-to-end processing and analysis of highly multiplexed immunofluorescence imaging data.
Built on xarray and dask, with seamless integration into the scverse ecosystem.
www.biorxiv.org/content/10.1...
We introduce 𝐬𝐩𝐚𝐭𝐢𝐚𝐥𝐩𝐫𝐨𝐭𝐞𝐨𝐦𝐢𝐜𝐬, a Python package for end-to-end processing and analysis of highly multiplexed immunofluorescence imaging data.
Built on xarray and dask, with seamless integration into the scverse ecosystem.
www.biorxiv.org/content/10.1...
May 5, 2025 at 11:30 AM
New preprint out!
We introduce 𝐬𝐩𝐚𝐭𝐢𝐚𝐥𝐩𝐫𝐨𝐭𝐞𝐨𝐦𝐢𝐜𝐬, a Python package for end-to-end processing and analysis of highly multiplexed immunofluorescence imaging data.
Built on xarray and dask, with seamless integration into the scverse ecosystem.
www.biorxiv.org/content/10.1...
We introduce 𝐬𝐩𝐚𝐭𝐢𝐚𝐥𝐩𝐫𝐨𝐭𝐞𝐨𝐦𝐢𝐜𝐬, a Python package for end-to-end processing and analysis of highly multiplexed immunofluorescence imaging data.
Built on xarray and dask, with seamless integration into the scverse ecosystem.
www.biorxiv.org/content/10.1...